Nuts and Bolts of CF3 and CH 3 NMR Toward the Understanding of Conformational Exchange of GPCRs

Targeted Activation of GPCR-Mediated Ca2+ Signaling Drives Enhanced Cartilage-Like Matrix Formation

Intracellular calcium ([Ca²⁺]_i) signaling is a critical regulator of chondrogenesis, chondrocyte differentiation, and cartilage development. Calcium (Ca²⁺) signaling is known to direct processes that govern chondrocyte gene expression, protein synthesis, cytoskeletal remodeling, and cell fate. Control of chondrocyte/chondroprogenitor Ca²⁺ signaling has been attempted through mechanical and/or pharmacological activation of endogenous Ca²⁺ signaling transducers; however, such approaches can lack specificity and/or precision regarding Ca²⁺ activation mechanisms. Synthetic signaling platforms permitting precise and selective Ca²⁺ signal transduction can improve dissection of the roles that [Ca²⁺]_i signaling play in chondrocyte behavior. One such platform is the chemogenetic hM3Dq DREADD (designer receptor exclusively activated by designer drugs) that activates [Ca²⁺]_i signaling via the Gα_q-PLCβ-IP₃-ER pathway upon clozapine N-oxide (CNO) administration. We previously demonstrated hM3Dq's ability to precisely and synthetically initiate robust [Ca²⁺]_i transients and oscillatory [Ca²⁺]_i signaling in chondrocyte-like ATDC5 cells. Here, we investigate the effects that long-term CNO stimulatory culture have on hM3Dq [Ca²⁺]_i signaling dynamics, proliferation, and protein deposition in 2D ATDC5 cultures. Long-term culturing under repeated CNO stimulation modified the temporal dynamics of hM3Dq [Ca²⁺]_i signaling, increased cell proliferation, and enhanced matrix production in a CNO dose- and frequency-dependent manner, and triggered the formation of cell condensations that developed aligned, anisotropic neotissue structures rich in cartilaginous proteoglycans and collagens, all in the absence of differentiation inducers. This study demonstrated Gα_q-GPCR-mediated [Ca²⁺]_i signaling involvement in chondroprogenitor proliferation and cartilage-like matrix production, and established hM3Dq as a powerful tool for elucidating the role of GPCR-mediated Ca²⁺ signaling in chondrogenesis and chondrocyte differentiation.

Targeted Gq-GPCR activation drives ER-dependent calcium oscillations in chondrocytes

The temporal dynamics of calcium signaling are critical regulators of chondrocyte homeostasis and chondrogenesis. Calcium oscillations regulate differentiation and anabolic processes in chondrocytes and their precursors. Attempts to control chondrocyte calcium signaling have been achieved through mechanical perturbations and synthetic ion channel modulators. However, such stimuli can lack both local and global specificity and precision when evoking calcium signals. Synthetic signaling platforms can more precisely and selectively activate calcium signaling, enabling improved dissection of the roles of intracellular calcium ([Ca²⁺]_i) in chondrocyte behavior. One such platform is hM3Dq, a chemogenetic DREADD (Designer Receptors Exclusively Activated by Designer Drugs) that activates calcium signaling via the Gα_q-PLCβ-IP₃-ER pathway upon administration of clozapine N-oxide (CNO). We previously described the first-use of hM3Dq to precisely mediate targeted, synthetic calcium signals in chondrocyte-like ATDC5 cells. Here, we generated stably expressing hM3Dq-ATDC5 cells to investigate the dynamics of Gα_q-GPCR calcium signaling in depth. CNO drove robust calcium responses in a temperature- and concentration-dependent (1 pM-100 μM) manner and elicited elevated levels of oscillatory calcium signaling above 10 nM. hM3Dq-mediated calcium oscillations in ATDC5 cells were reliant on ER calcium stores for both initiation and sustenance, and the downregulation and recovery dynamics of hM3Dq after CNO stimulation align with traditionally reported GPCR recycling kinetics. This study successfully generated a stable hM3Dq cell line to precisely drive Gα_q-GPCR-mediated and ER-dependent oscillatory calcium signaling in ATDC5 cells and established a novel tool to elucidate the role that GPCR-mediated calcium signaling plays in chondrocyte biology, cartilage pathology, and cartilage tissue engineering.

The role of NMR in leveraging dynamics and entropy in drug design

Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.

Expression and Purification of a Functional E. coli 13CH3-Methionine-Labeled Thermostable Neurotensin Receptor 1 Variant for Solution NMR Studies

Escherichia coli (E. coli) is the most widely used expression host for recombinant proteins due to high expression yields and straightforward molecular cloning. Directed evolution of G protein-coupled receptors (GPCRs) has made several of these difficult to express membrane proteins amenable to prokaryotic expression. Here, we describe a protocol for near complete ¹³CH₃-methionine labeling of a thermostable neurotensin receptor 1 (enNTS₁) variant in E. coli for solution NMR-based dynamics studies. Our expression strategy utilizes methionine biosynthesis pathway inhibition forcing E. coli to incorporate exogenous methionine with 96% efficiency at expression levels of 2.6 mg enNTS₁ per liter of expression culture containing 50 mg of ¹³CH₃-methionine. We also provide a 3-step purification protocol that produces final yields of 0.6 mg of functional Apo-state enNTS₁.

Solution NMR spectroscopy of GPCRs: Residue-specific labeling strategies with a focus on 13C-methyl methionine labeling of the atypical chemokine receptor ACKR3

The past decade has witnessed remarkable progress in the determination of G protein-coupled receptor (GPCR) structures, profoundly expanding our understanding of how GPCRs recognize ligands, become activated, and interact with intracellular signaling components. In recent years, numerous studies have used solution nuclear magnetic resonance (NMR) spectroscopy to investigate GPCRs, providing fundamental insights into GPCR conformational changes, allostery, dynamics, and other facets of GPCR function are challenging to study using other structural techniques. Despite these advantages, NMR-based studies of GPCRs are few relative to the number of published structures, due in part to the challenges and limitations of NMR for the characterization of large membrane proteins. Several studies have circumvented these challenges using a variety of isotopic labeling strategies, including side chain derivatization and metabolic incorporation of NMR-active nuclei. In this chapter, we provide an overview of different isotopic labeling strategies and describe an in-depth protocol for the expression, purification, and NMR studies of the chemokine GPCR atypical chemokine receptor 3 (ACKR3) via ¹³CH₃-methionine incorporation. The goal of this chapter is to provide a resource to the GPCR community for those interested in pursuing NMR studies of GPCRs.

GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures

The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.

Forbidden Coherence Transfer of 19F Nuclei to Quantitatively Measure the Dynamics of a CF₃-Containing Ligand in Receptor-Bound States

The dynamic property of a ligand in the receptor-bound state is an important metric to characterize the interactions in the ligand–receptor interface, and the development of an experimental strategy to quantify the amplitude of motions in the bound state is of importance to introduce the dynamic aspect into structure-guided drug development (SGDD). Fluorine modifications are frequently introduced at the hit-to-lead optimization stage to enhance the binding potency and other characteristics of a ligand. However, the effects of fluorine modifications are generally difficult to predict, owing to the pleiotropic nature of the interactions. In this study, we report an NMR-based approach to experimentally evaluate the local dynamics of trifluoromethyl (CF₃)-containing ligands in the receptor-bound states. For this purpose, the forbidden coherence transfer (FCT) analysis, which has been used to study the dynamics of methyl moieties in proteins, was extended to the ¹⁹F nuclei of CF₃-containing ligands. By applying this CF₃–FCT analysis to a model interaction system consisting of a ligand, AST-487, and a receptor, p38α, we successfully quantified the amplitude of the CF₃ dynamics in the p38α-bound state. The strategy would bring the CF₃-containing ligands within the scope of dynamic SGDD to improve the affinity and specificity for the drug-target receptors.